18-46665492-C-T

Position:

• chr18-46665492-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_935430.4(LOC105372096):​n.716G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,014 control chromosomes in the GnomAD database, including 4,637 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4637 hom., cov: 31)
• Consequence: LOC105372096 XR_935430.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

Genes affected

LOC105372096 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372096	XR_935430.4	n.716G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36649 AN: 151896 Hom.: 4637 Cov.: 31

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.243

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.241 AC: 36665 AN: 152014 Hom.: 4637 Cov.: 31 AF XY: 0.240 AC XY: 17864 AN XY: 74306

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.240

Alfa AF: 0.262 Hom.: 10959

Bravo AF: 0.231

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs430374; hg19: chr18-44245455;